Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015625.1 Corchorus olitorius cultivar O-4 contig15658, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 115964
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:731 original size:203 final size:202
Alignment explanation
Indices: 328--734 Score: 692
Period size: 203 Copynumber: 2.0 Consensus size: 202
318 TATCAATGAT
*
328 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTATTAACAAAGTTGTAGTGAATAAGATA
1 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
*
393 CAACACATTATTATTATATATAAAACTATACCAAAAAAAAAGTAGTTGAACATTAGTGGTTGATT
66 CAACACATTACTATTATATATAAAACTATACC-AAAAAAAAGTAGTTGAACATTAGTGGTTGATT
**
458 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTTA
130 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
523 TTTATTTA
195 TTTATTTA
531 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
1 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
* *
596 CAATACATTACTATTATATATAATAGAACTATACC-AAAAAAATTAGTTGAACATTAGTGGTTGA
66 CAACACATTACTATTATATAT-A-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGA
**
660 TTTATTTTATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
128 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
724 GATTTATTTA
193 GATTTATTTA
734 T
1 T
735 TCTTAGGGAA
Statistics
Matches: 193, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
203 99 0.51
204 84 0.44
205 1 0.01
206 9 0.05
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (202 bp):
TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
CAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTT
ATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGAT
TTATTTA
Found at i:839 original size:25 final size:24
Alignment explanation
Indices: 805--851 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
795 ACGTTTGCAC
805 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
830 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
852 TGTATGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:900 original size:39 final size:40
Alignment explanation
Indices: 842--922 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
832 ATACCTAAGA
* * *
842 ATTTAATTAATGTATGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
*
881 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
921 AT
1 AT
923 AGCAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
Found at i:9952 original size:31 final size:31
Alignment explanation
Indices: 9917--9985 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
9907 AAATTGACTC
9917 TAGGGACGGATTTGAG-CCGATTTTACAATGT
1 TAGGGACGGATTTGAGTCCGA-TTTACAATGT
* ** *
9948 TAGGGACTGATTTGAGTTGGATTTATAATGT
1 TAGGGACGGATTTGAGTCCGATTTACAATGT
9979 TAGGGAC
1 TAGGGAC
9986 TTAATTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (31 bp):
TAGGGACGGATTTGAGTCCGATTTACAATGT
Found at i:10520 original size:17 final size:17
Alignment explanation
Indices: 10483--10520 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10473 ATCACCCCTC
* *
10483 AGATGACTGGTGCTCTT
1 AGATGACTGGTGATCTG
10500 AGATGACTGGTGATCTG
1 AGATGACTGGTGATCTG
10517 AGAT
1 AGAT
10521 TACCTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (17 bp):
AGATGACTGGTGATCTG
Found at i:11288 original size:14 final size:14
Alignment explanation
Indices: 11269--11298 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11259 AGTGTACAAT
11269 TAATTACATATACA
1 TAATTACATATACA
11283 TAATTACATATACA
1 TAATTACATATACA
11297 TA
1 TA
11299 TTAATGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTACATATACA
Found at i:11946 original size:27 final size:27
Alignment explanation
Indices: 11876--11950 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
11866 GTCTATACTC
* * *
11876 TTTTTTTTCATCTTTTATTTTATTTATA
1 TTTTTTTTTA-CTTTTGTTTTATTAATA
* * *
11904 TTTATTTATA-TATTTGTTTTATTAATG
1 TTTTTTTTTACT-TTTGTTTTATTAATA
11931 TTTTTTTTTACTTTTGTTTT
1 TTTTTTTTTACTTTTGTTTT
11951 GTTTTTTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
26 1 0.03
27 28 0.76
28 8 0.22
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTACTTTTGTTTTATTAATA
Found at i:12815 original size:75 final size:76
Alignment explanation
Indices: 12673--12823 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 76
12663 TTAACTAAAT
** **
12673 TGAGAAAAGACCAAAACGGGGCGAAAAAGGTTCTCCCACATTAAAAGTTGATGGGAGCTATTGGT
1 TGAGAAAAGACCAAAACGGGGCGAAAAAGGTTCTCCCACATTAAAAGTTGATGAAAGCTATCAGT
12738 AATTTCCAGAG
66 AATTTCCAGAG
* * * * * *
12749 TGAGAAAATACCAAAATGGGGCG-AAAAGGTTCTGCCACGTTACAAGTTGATTAAAGCTATCAGT
1 TGAGAAAAGACCAAAACGGGGCGAAAAAGGTTCTCCCACATTAAAAGTTGATGAAAGCTATCAGT
*
12813 AATTTCTAGAG
66 AATTTCCAGAG
12824 GGTATTCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
75 43 0.67
76 21 0.33
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (76 bp):
TGAGAAAAGACCAAAACGGGGCGAAAAAGGTTCTCCCACATTAAAAGTTGATGAAAGCTATCAGT
AATTTCCAGAG
Found at i:13717 original size:22 final size:22
Alignment explanation
Indices: 13659--13876 Score: 120
Period size: 22 Copynumber: 9.7 Consensus size: 22
13649 AACTTGCAGA
13659 TTATCAAAATTTCATAGTATGCATGG
1 TTATCAAAATTTCATA--ATG--TGG
* *
13685 CTACCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAATGTGG
* *
13707 TTCTCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAATGTGG
*
13729 TTA-CAAAAATTTCAT-A-GAAGG
1 TTATC-AAAATTTCATAATG-TGG
* * *
13750 TAATCAAAATTTCATATTGTGC
1 TTATCAAAATTTCATAATGTGG
* * *
13772 TTATCAAAATTTCATAGTGAGA
1 TTATCAAAATTTCATAATGTGG
* * ** **
13794 TTAACGAAA-TTCTATAGGGAAG
1 TTATCAAAATTTC-ATAATGTGG
* ** *
13816 TTATCAATATTTCATAGGGAGG
1 TTATCAAAATTTCATAATGTGG
* *
13838 TTATCAAAATTTCAATAGTATGG
1 TTATCAAAATTTC-ATAATGTGG
*
13861 TTATCCAAATTTCATA
1 TTATCAAAATTTCATA
13877 GTGTACCAAA
Statistics
Matches: 153, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 19 0.12
22 94 0.61
23 22 0.14
24 3 0.02
26 14 0.09
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:13804 original size:65 final size:65
Alignment explanation
Indices: 13689--13856 Score: 153
Period size: 65 Copynumber: 2.6 Consensus size: 65
13679 GCATGGCTAC
* * * * *
13689 CAAAATTTCATAATGTGGTTCTCAAAATTTTATAATGTGGTTACAAAAATT-TCATA-GAAGGTA
1 CAAAATTTCATAATGTGGTTATCAAAATTTCATAGTGAGATTACAAAAATTCT-ATAGGAA-GTA
13752 AT
64 AT
* * * *
13754 CAAAATTTCATATTGTGCTTATCAAAATTTCATAGTGAGATTA-ACGAAATTCTATAGGGAAGTT
1 CAAAATTTCATAATGTGGTTATCAAAATTTCATAGTGAGATTACA-AAAATTCTATA-GGAAGTA
13818 AT
64 AT
* ** *
13820 CAATATTTCATAGGGAGGTTATCAAAATTTCAATAGT
1 CAAAATTTCATAATGTGGTTATCAAAATTTC-ATAGT
13857 ATGGTTATCC
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 1 0.01
65 44 0.52
66 31 0.37
67 8 0.10
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (65 bp):
CAAAATTTCATAATGTGGTTATCAAAATTTCATAGTGAGATTACAAAAATTCTATAGGAAGTAAT
Found at i:14006 original size:21 final size:22
Alignment explanation
Indices: 13982--14041 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
13972 AGTGTGGTTT
*
13982 TCAAAATTTCATAGGATGA-TA
1 TCAAAATTTCATAGGATCACTA
*
14003 TCAAAATTTCATAGTGGTCACTA
1 TCAAAATTTCATAG-GATCACTA
*
14026 TCAAAGTTTCATAGGA
1 TCAAAATTTCATAGGA
14042 GGTTACCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 14 0.42
22 4 0.12
23 15 0.45
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAGGATCACTA
Found at i:14107 original size:22 final size:21
Alignment explanation
Indices: 13982--14107 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 21
13972 AGTGTGGTTT
13982 TCAAAATTTCATAGGATGA-TA
1 TCAAAATTTCATAGGA-GATTA
*
14003 TCAAAATTTCATAGTG-GTCACTA
1 TCAAAATTTCATAG-GAG--ATTA
* *
14026 TCAAAGTTTCATAGGAGGTTA
1 TCAAAATTTCATAGGAGATTA
* *
14047 CCCAATTAATTTCTTAGG-GAAGTTA
1 -TCAA--AATTTCATAGGAG-A-TTA
*
14072 TCAAAATAAT-ATAGCGAGATTA
1 TCAAAAT-TTCATAG-GAGATTA
14094 TCAAAATTTCATAG
1 TCAAAATTTCATAG
14108 TAAGTAGGAG
Statistics
Matches: 80, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
20 1 0.01
21 17 0.21
22 26 0.32
23 20 0.25
24 13 0.16
25 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TCAAAATTTCATAGGAGATTA
Found at i:15027 original size:1 final size:1
Alignment explanation
Indices: 15021--15045 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
15011 AATTGGTTGA
15021 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
15046 CAAGTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:36308 original size:10 final size:10
Alignment explanation
Indices: 36293--36318 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36283 AATTAACAAG
36293 ATAATTAGAA
1 ATAATTAGAA
36303 ATAATTAGAA
1 ATAATTAGAA
36313 ATAATT
1 ATAATT
36319 TCTGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (10 bp):
ATAATTAGAA
Found at i:40953 original size:14 final size:14
Alignment explanation
Indices: 40934--40963 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40924 CGAATTGACA
40934 AACAGAATAATGAT
1 AACAGAATAATGAT
40948 AACAGAATAATGAT
1 AACAGAATAATGAT
40962 AA
1 AA
40964 TAATAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (14 bp):
AACAGAATAATGAT
Found at i:41454 original size:14 final size:14
Alignment explanation
Indices: 41435--41463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41425 CTGACAAGTG
41435 ACAACAGATTGTTA
1 ACAACAGATTGTTA
41449 ACAACAGATTGTTA
1 ACAACAGATTGTTA
41463 A
1 A
41464 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ACAACAGATTGTTA
Found at i:42655 original size:17 final size:17
Alignment explanation
Indices: 42629--42670 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
42619 GCAGCTCCCT
*
42629 ATGTCTTTCTACCCTCC
1 ATGTCCTTCTACCCTCC
42646 ATGTCCTTCTACCCTCC
1 ATGTCCTTCTACCCTCC
42663 ATGTCCTT
1 ATGTCCTT
42671 TTATGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.40, G:0.07, T:0.40
Consensus pattern (17 bp):
ATGTCCTTCTACCCTCC
Found at i:45162 original size:23 final size:23
Alignment explanation
Indices: 45119--45167 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
45109 AAAAATTTAG
** *
45119 CTTTATAGAGATGTTTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
45142 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
45165 CTT
1 CTT
45168 AGAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:48069 original size:20 final size:20
Alignment explanation
Indices: 48044--48113 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
48034 TTGGCCTCCA
48044 TCGCGGCCATTACGTAAGGG
1 TCGCGGCCATTACGTAAGGG
48064 TCGCGGCCATTACGTAAGGG
1 TCGCGGCCATTACGTAAGGG
48084 TCGCGGCCATTACGTAAGGG
1 TCGCGGCCATTACGTAAGGG
48104 TCGCGGCCAT
1 TCGCGGCCAT
48114 GACACATGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.20
Consensus pattern (20 bp):
TCGCGGCCATTACGTAAGGG
Found at i:50478 original size:32 final size:32
Alignment explanation
Indices: 50442--50507 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
50432 TTGAGTTAGG
* *
50442 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTAATTCGGGT
*
50474 TCGGGTTAATTTTGGATCAGGTTAATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTAATTCGGGT
50506 TC
1 TC
50508 AGACTGGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (32 bp):
TCGGGTTAAATTTGGATCAGGTTAATTCGGGT
Found at i:50509 original size:16 final size:16
Alignment explanation
Indices: 50445--50509 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
50435 AGTTAGGTCG
*
50445 GGTTAAATTTGGG-TCA
1 GGTT-AATTCGGGTTCA
* *
50461 GGTTGATTCGGGTTCG
1 GGTTAATTCGGGTTCA
** *
50477 GGTTAATTTTGGATCA
1 GGTTAATTCGGGTTCA
50493 GGTTAATTCGGGTTCA
1 GGTTAATTCGGGTTCA
50509 G
1 G
50510 ACTGGATTTT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 6 0.16
16 31 0.84
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.38
Consensus pattern (16 bp):
GGTTAATTCGGGTTCA
Found at i:52717 original size:30 final size:30
Alignment explanation
Indices: 52643--53145 Score: 670
Period size: 30 Copynumber: 16.7 Consensus size: 30
52633 GCTAATATAT
* *
52643 ATTGACACCAAAAGTTGTCAATGGTCTTACA
1 ATTGACACCAGAAGTTGTC-ATGGTCTTGCA
* * *
52674 AATGACACTAGAAGTTGTCATGCTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
*
52704 ATTGACACCAGAAGTTGTCATGCTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* *
52734 ATTGACACCAGAACTTGTCAATGATCTTGCA
1 ATTGACACCAGAAGTTGTC-ATGGTCTTGCA
*
52765 ATTGACACCAGAAGTTG---GGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
*
52792 AATGACACCAGAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* *
52822 AATGACACCAGAAGTTGTCATGGCCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
*
52852 AATGACACCAGAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
52882 ATTGACACCAGAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
*
52912 ATTAACACCAGAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
*
52942 ATTGACACCATAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
**
52972 ATTGACACCAGAACCTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* *
53002 ATTGACACCAGAAGCTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* * * *
53032 ATTGACACTAGAAGCTGTCATGATGTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* *
53062 ATTGACACCAGAAGCTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGGTCTTGCA
* * ** * *
53092 ATTAACACCATAAGTTGTCATAATTTTATTCA
1 ATTGACACCAGAAGTTGTCAT-GGTCT-TGCA
53124 ATTGACACCAGAAGTTGTCATG
1 ATTGACACCAGAAGTTGTCATG
53146 ATAAATTTCC
Statistics
Matches: 427, Mismatches: 39, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.06
30 337 0.79
31 44 0.10
32 22 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGGTCTTGCA
Found at i:53132 original size:32 final size:31
Alignment explanation
Indices: 52676--53209 Score: 220
Period size: 30 Copynumber: 17.6 Consensus size: 31
52666 GTCTTACAAA
* ** * *
52676 TGACACTAGAAGTTGTCAT-GCTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
** * *
52706 TGACACCAGAAGTTGTCAT-GCTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* * * *
52736 TGACACCAGAACTTGTCAATGA-TCTTGCAAT
1 TGACACCAGAAGTTGTC-ATAATTTTTTCAAT
*** * * *
52767 TGACACCAGAAGTTG----GGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
** * * *
52794 TGACACCAGAAGTTGTCAT-GGTCTTGCAAA
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
**** * *
52824 TGACACCAGAAGTTGTCAT-GGCCTTGCAAA
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
** * *
52854 TGACACCAGAAGTTGTCAT-GGTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
** * *
52884 TGACACCAGAAGTTGTCAT-GGTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* ** * *
52914 TAACACCAGAAGTTGTCAT-GGTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* ** * *
52944 TGACACCATAAGTTGTCAT-GGTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
** ** * *
52974 TGACACCAGAACCTGTCAT-GGTCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* * * *
53004 TGACACCAGAAGCTGTCATGA-TCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* * * * *
53034 TGACACTAGAAGCTGTCATGA-TGTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* * * *
53064 TGACACCAGAAGCTGTCATGA-TCTTGCAAT
1 TGACACCAGAAGTTGTCATAATTTTTTCAAT
* *
53094 TAACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATTTT-TTCAAT
** *
53126 TGACACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCAT-A-ATTTTTTCAAT
* ** *
53159 AGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATTTT-TTCAAT
53191 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
53210 GATAAATTTC
Statistics
Matches: 448, Mismatches: 43, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.00
27 23 0.05
30 327 0.73
31 30 0.07
32 43 0.10
33 21 0.05
34 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
TGACACCAGAAGTTGTCATAATTTTTTCAAT
Found at i:53196 original size:65 final size:61
Alignment explanation
Indices: 52880--53267 Score: 289
Period size: 60 Copynumber: 6.4 Consensus size: 61
52870 CATGGTCTTG
* ** * ** * *
52880 CAATTGACACCAGAAGTTGTCATGGTCTTGCAATTAACACCAGAAGTTGTCAT-GGTCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTGCAA-TAACACTTGAAGATGTCATAATTTTATT
* * * ** ** ** * *
52940 CAATTGACACCATAAGTTGTCATGGTCTTGCAATTGACACCAGAACCTGTCAT-GGTCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTGCAA-TAACACTTGAAGATGTCATAATTTTATT
* * * * * * *
53000 CAATTGACACCAGAAGCTGTCATGATCTTGCAATTGACACTAGAAGCTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTGCAA-TAACACTTGAAGATGTCATAATTTTATT
* * *
53060 CAATTGACACCAGAAGCTGTCATGATCTTGCAATTAACACCAT-AAGTTGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTGCAA-TAACA-CTTGAAGATGTCATAATTTTATT
* *
53122 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTGCAATA-ACACTTGAAGATGTCATAATTTTATT
***
53187 CAATTGACACCAGAAGTTGTCATGA---T--AA-ATTTCTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTGCAATAACACTTGAAGATGTCATAATTTTATT
*
53242 CAATTGACACCAGAAGTCGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
53268 TTTACCTTTC
Statistics
Matches: 291, Mismatches: 27, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
55 47 0.16
56 1 0.00
57 2 0.01
59 1 0.00
60 156 0.54
61 3 0.01
62 26 0.09
64 4 0.01
65 51 0.18
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (61 bp):
CAATTGACACCAGAAGTTGTCATGATCTTGCAATAACACTTGAAGATGTCATAATTTTATT
Found at i:53248 original size:55 final size:55
Alignment explanation
Indices: 53164--53267 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
53154 CCAATAGACA
*
53164 CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTT
1 CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTCGTCATGATAAATTT
53219 CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTCGTCATGAT
1 CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTCGTCATGAT
53268 TTTACCTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (55 bp):
CTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGTCGTCATGATAAATTT
Found at i:53811 original size:15 final size:16
Alignment explanation
Indices: 53787--53826 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
53777 AGAGGTTGAA
*
53787 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
53802 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
53818 AGAAAACAA
1 AGAAAACAA
53827 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:64346 original size:83 final size:84
Alignment explanation
Indices: 64251--64405 Score: 258
Period size: 83 Copynumber: 1.9 Consensus size: 84
64241 AGACTTTTTT
* * *
64251 TTATCTCTTTATAACTATTTTATTTTTACCTTTTTACTA-TTTAATTAAAAAACTTAGATATATT
1 TTATCTCCTTATAACTATTTTACTTTTACCCTTTTACTATTTTAATTAAAAAACTTAGATATATT
64315 AGAATTTCTTAATTAAAAC
66 AGAATTTCTTAATTAAAAC
**
64334 TTATCTCCTTATAACTATTTTACTTTTACCCTTTTACTATTTTAATTGCAAAACTTAGATATATT
1 TTATCTCCTTATAACTATTTTACTTTTACCCTTTTACTATTTTAATTAAAAAACTTAGATATATT
64399 AGAATTT
66 AGAATTT
64406 TTCAAATAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 36 0.55
84 30 0.45
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (84 bp):
TTATCTCCTTATAACTATTTTACTTTTACCCTTTTACTATTTTAATTAAAAAACTTAGATATATT
AGAATTTCTTAATTAAAAC
Found at i:65897 original size:14 final size:15
Alignment explanation
Indices: 65868--65900 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
65858 ATACTTTGGA
*
65868 ATTTTGATCTTTTTT
1 ATTTTGATCATTTTT
65883 ATTTT-ATCATTTTT
1 ATTTTGATCATTTTT
65897 ATTT
1 ATTT
65901 AGGATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (15 bp):
ATTTTGATCATTTTT
Found at i:70086 original size:10 final size:12
Alignment explanation
Indices: 70061--70117 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
70051 TTATGCACCC
70061 AAAACATTTATT
1 AAAACATTTATT
*
70073 AAAACATTT-TA
1 AAAACATTTATT
70084 AAAATCATTTATGT
1 AAAA-CATTTAT-T
* *
70098 AAAAC-TGTAAT
1 AAAACATTTATT
70109 AAAACATTT
1 AAAACATTT
70118 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 11 0.31
12 19 0.53
13 2 0.06
14 4 0.11
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (12 bp):
AAAACATTTATT
Found at i:70116 original size:24 final size:23
Alignment explanation
Indices: 70061--70117 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
70051 TTATGCACCC
*
70061 AAAACATTTATTAAAACATTTTAA
1 AAAACATTTATTAAAACA-TGTAA
*
70085 AAATCATTTATGTAAAAC-TGTAA
1 AAAACATTTAT-TAAAACATGTAA
70108 TAAAACATTT
1 -AAAACATTT
70118 CCTCAACGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.14
24 18 0.64
25 6 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAACATTTATTAAAACATGTAA
Found at i:71368 original size:35 final size:35
Alignment explanation
Indices: 71293--71374 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 35
71283 CCAAGCTTGA
71293 GCGCTGGGCCATGGCTGGCCCGCGCACCAGGCCTGG
1 GCGCTGGGCCATGGCTGGCCCGCG-ACCAGGCCTGG
*
71329 GCGCTGGGCCATGCGCTGGCCCGCG-CCTGGCCTGG
1 GCGCTGGGCCATG-GCTGGCCCGCGACCAGGCCTGG
71364 GCGCTTGGGCC
1 GCGC-TGGGCC
71375 GCGCCAGGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 13 0.30
36 19 0.44
37 11 0.26
ACGTcount: A:0.05, C:0.39, G:0.43, T:0.13
Consensus pattern (35 bp):
GCGCTGGGCCATGGCTGGCCCGCGACCAGGCCTGG
Found at i:71384 original size:24 final size:23
Alignment explanation
Indices: 71341--71387 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
71331 GCTGGGCCAT
*
71341 GCGCTGGCCCGCGCCTGGCCTGG
1 GCGCTGGCCCGCGCCAGGCCTGG
*
71364 GCGCTTGGGCCGCGCCAGGCCTGG
1 GCGC-TGGCCCGCGCCAGGCCTGG
71388 CCCAAGCGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.02, C:0.40, G:0.45, T:0.13
Consensus pattern (23 bp):
GCGCTGGCCCGCGCCAGGCCTGG
Found at i:72697 original size:27 final size:27
Alignment explanation
Indices: 72667--72751 Score: 118
Period size: 27 Copynumber: 3.1 Consensus size: 27
72657 ATTAACTCAC
72667 AAAGCAATGATCCTGAATAGGATT-GA
1 AAAGCAATGATCCTGAATAGGATTCGA
*
72693 GAAAGCAATGATCCTGAATAGGATTCTA
1 -AAAGCAATGATCCTGAATAGGATTCGA
* *
72721 AAAGCAATGATCCTGAACATGATTCTGA
1 AAAGCAATGATCCTGAATAGGATTC-GA
72749 AAA
1 AAA
72752 TGACAGATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 47 0.90
28 5 0.10
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (27 bp):
AAAGCAATGATCCTGAATAGGATTCGA
Found at i:72865 original size:77 final size:79
Alignment explanation
Indices: 72721--72900 Score: 247
Period size: 78 Copynumber: 2.3 Consensus size: 79
72711 TAGGATTCTA
* * *
72721 AAAGCAATGATCCTGAACATGATTCTGAAAATGACAGATAAAGTAATGATCCTGAATAAAATCCT
1 AAAGCAATGATCCTGAATAGGATTCTGAAAATGACAGATAAAGCAATGATCCTGAATAAAATCCT
* *
72786 GAAATTGA-TTGAT
66 GAAATTCACTCGAT
* ** *
72799 AAAGCGATGATCCTGAATAGGATTCTG-AAATGACAGATAAAGCAATGATCCTGAATAGGATTCT
1 AAAGCAATGATCCTGAATAGGATTCTGAAAATGACAGATAAAGCAATGATCCTGAATAAAATCCT
72863 GAAATTCACTCGAT
66 GAAATTCACTCGAT
* *
72877 AAAGTAATGATCCTGAGTAGGATT
1 AAAGCAATGATCCTGAATAGGATT
72901 GAAATTGACT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 40 0.45
78 49 0.55
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (79 bp):
AAAGCAATGATCCTGAATAGGATTCTGAAAATGACAGATAAAGCAATGATCCTGAATAAAATCCT
GAAATTCACTCGAT
Found at i:72904 original size:38 final size:40
Alignment explanation
Indices: 72721--72910 Score: 221
Period size: 39 Copynumber: 4.9 Consensus size: 40
72711 TAGGATTCTA
* * *
72721 AAAGCAATGATCCTGAACATGATTCTGAAAATGAC-AGAT
1 AAAGCAATGATCCTGAATAGGATTCTGAAATTGACTAGAT
* ** * *
72760 AAAGTAATGATCCTGAATAAAATCCTGAAATTGA-TTGAT
1 AAAGCAATGATCCTGAATAGGATTCTGAAATTGACTAGAT
*
72799 AAAGCGATGATCCTGAATAGGATTCTGAAA-TGAC-AGAT
1 AAAGCAATGATCCTGAATAGGATTCTGAAATTGACTAGAT
* *
72837 AAAGCAATGATCCTGAATAGGATTCTGAAATTCACTCGAT
1 AAAGCAATGATCCTGAATAGGATTCTGAAATTGACTAGAT
* *
72877 AAAGTAATGATCCTGAGTAGGA-T-TGAAATTGACT
1 AAAGCAATGATCCTGAATAGGATTCTGAAATTGACT
72911 TGTAAAAAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
38 45 0.35
39 60 0.47
40 23 0.18
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (40 bp):
AAAGCAATGATCCTGAATAGGATTCTGAAATTGACTAGAT
Found at i:73329 original size:141 final size:140
Alignment explanation
Indices: 73010--73338 Score: 498
Period size: 140 Copynumber: 2.3 Consensus size: 140
73000 GTCAGAATTA
* * *
73010 ATACCCGGAGGTTTTATCAGAATTAATACCTGGAGATTTCTGAAATTGTGCCCGGAGGTCTTACA
1 ATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
* * * * **
73075 AATGCAAACTCGACCTTGAGCAAGGTTTTTGATATTTAAACGCAACTTTGATTAACAATTTGGTG
66 AATGCAAACTCGACCTTGAACAAGGTTTTTGAAACTTAAACGCAACTTTGATTAACAACTTAATG
73140 CAATGAGGTG
131 CAATGAGGTG
*
73150 ATACCCGGAGGATTTATCAGAATTAATACCCGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
1 ATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
* *
73215 AATGCAAACTCGACCTTGAACAAGGTTTATTGAAACTTAAGCGCAGCTTTGATTAACAACTTAAT
66 AATGCAAACTCGACCTTGAACAAGGTTT-TTGAAACTTAAACGCAACTTTGATTAACAACTTAAT
* *
73280 G-AGCTGAGGTT
130 GCA-ATGAGGTG
*
73291 ATACCCGGAGGATTTATCATAATTAATACCCGGAGGTTTCTGAAATTG
1 ATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTG
73339 CAAACTCAAC
Statistics
Matches: 171, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
140 89 0.52
141 82 0.48
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (140 bp):
ATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
AATGCAAACTCGACCTTGAACAAGGTTTTTGAAACTTAAACGCAACTTTGATTAACAACTTAATG
CAATGAGGTG
Found at i:74826 original size:12 final size:12
Alignment explanation
Indices: 74799--74827 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
74789 TTCTTCATCT
74799 TTTTC-CTTTCC
1 TTTTCACTTTCC
74810 TTTTCACTTTCC
1 TTTTCACTTTCC
74822 TTTTCA
1 TTTTCA
74828 AATTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTCACTTTCC
Found at i:75347 original size:19 final size:19
Alignment explanation
Indices: 75299--75348 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
75289 ACCAAGTGCC
**
75299 TTTCTCTTCTTTTTTCTTTT
1 TTTCTCTT-TTTTTTCACTT
75319 TTTCAT-TTTTTTTTCACTT
1 TTTC-TCTTTTTTTTCACTT
75338 TTTCTCTTTTT
1 TTTCTCTTTTT
75349 CGATGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 18 0.69
20 6 0.23
21 1 0.04
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTCTTTTTTTTCACTT
Found at i:81581 original size:13 final size:13
Alignment explanation
Indices: 81565--81607 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
81555 TATCTGACTG
*
81565 TTTGGTTTATTAT
1 TTTGGTTTATTAC
*
81578 TTTGATTTATTAC
1 TTTGGTTTATTAC
*
81591 TTTGGTTTATGAC
1 TTTGGTTTATTAC
81604 TTTG
1 TTTG
81608 ATTATGATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.63
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:81804 original size:13 final size:12
Alignment explanation
Indices: 81786--81830 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
81776 ATTTTATTAC
81786 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
81799 TGTTTTATAAAT
1 TGTTTTATAAAT
*
81811 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
81825 TGTTTT
1 TGTTTT
81831 GGATGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:86066 original size:4 final size:4
Alignment explanation
Indices: 86052--86332 Score: 86
Period size: 4 Copynumber: 71.0 Consensus size: 4
86042 CCAAAAAAAG
* * * **
86052 ATTT TTTT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AACT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * * **
86099 A-TT ATCT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AACT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * * **
86145 A-TT ATCT ATTT ATTT A-CT ATTT ATCTT -TTT ATTT ATTA ATTT AGCT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * * ** ** *
86191 A-TT ATCT ATTT ATTT ACTATT ATCT ACTTT TTTT ACCT ACCT ATTT ATCT
1 ATTT ATTT ATTT ATTT A-T-TT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT
* * * ** * *
86241 AATT ATCT ATAT ACCT ATTT ATCTT -TTT ATTT ATCT A-TT ATTTT CACTT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT A-TTT -ATTT
*
86290 ATTT -TTCT ATTT ATTT ATTT ATTT ATCT A-TT ACTTT -TTT ATTT
1 ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT
86333 TAATATTTTT
Statistics
Matches: 199, Mismatches: 53, Indels: 50
0.66 0.18 0.17
Matches are distributed among these distances:
3 29 0.15
4 146 0.73
5 20 0.10
6 4 0.02
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (4 bp):
ATTT
Found at i:86083 original size:19 final size:19
Alignment explanation
Indices: 86061--86179 Score: 72
Period size: 19 Copynumber: 6.4 Consensus size: 19
86051 GATTTTTTTA
86061 TTTATTTACTATTTATATT
1 TTTATTTACTATTTATATT
* *
86080 TTTATTTATTAATTTA-ACT
1 TTTATTTACT-ATTTATATT
*
86099 ATTA--T-CTATTTAT-TT
1 TTTATTTACTATTTATATT
** *
86114 ACTATTTA-TATTTTTATT
1 TTTATTTACTATTTATATT
* *
86132 TATTAATTTAACTA-TTATCTA
1 T-TT-ATTT-ACTATTTATATT
*
86153 TTTATTTACTATTTATCTT
1 TTTATTTACTATTTATATT
86172 TTTATTTA
1 TTTATTTA
86180 TTAATTTAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
15 9 0.12
16 1 0.01
17 8 0.11
18 6 0.08
19 33 0.43
20 11 0.14
21 6 0.08
22 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTACTATTTATATT
Found at i:86089 original size:27 final size:27
Alignment explanation
Indices: 86053--86141 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
86043 CAAAAAAAGA
86053 TTTT-TTTATTTATTTACTATTTATAT
1 TTTTATTTATTTATTTACTATTTATAT
* *
86079 TTTTATTTATTAATTTAACTA-TTATCT
1 TTTTATTTATTTATTT-ACTATTTATAT
* * *
86106 ATTTATTTA-CTATTTA-TATTTTTAT
1 TTTTATTTATTTATTTACTATTTATAT
86131 TTATTAATTTA
1 TT-TT-ATTTA
86142 ACTATTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
24 2 0.04
25 6 0.12
26 10 0.20
27 28 0.56
28 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTTATTTATTTACTATTTATAT
Found at i:86126 original size:46 final size:46
Alignment explanation
Indices: 86059--86211 Score: 288
Period size: 46 Copynumber: 3.3 Consensus size: 46
86049 AAGATTTTTT
86059 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
86105 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
* *
86151 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
86197 TATTTATTTACTATT
1 TATTTATTTACTATT
86212 ATCTACTTTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
Found at i:86149 original size:27 final size:27
Alignment explanation
Indices: 86100--86187 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
86090 AATTTAACTA
* * *
86100 TTATCTATTTATTTACTATTTATATTT
1 TTATTTATTAATTTACTATTTATATAT
*
86127 TTATTTATTAATTTAACTA-TTATCTAT
1 TTATTTATTAATTT-ACTATTTATATAT
* * *
86154 TTATTTACT-ATTTATCTTTTTATTTAT
1 TTATTTATTAATTTA-CTATTTATATAT
*
86181 TAATTTA
1 TTATTTA
86188 GCTATTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 39 0.78
28 4 0.08
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTAATTTACTATTTATATAT
Found at i:86195 original size:27 final size:27
Alignment explanation
Indices: 86109--86206 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
86099 ATTATCTATT
* *
86109 TATTTA-CTATTTATATT-TTTATTTAT
1 TATTTATCTATTTAT-TTATTAATTTAC
* * *
86135 TAATTTAACTA-TTATCTATTTATTTAC
1 T-ATTTATCTATTTATTTATTAATTTAC
*
86162 TATTTATCTTTTTATTTATTAATTTAGC
1 TATTTATCTATTTATTTATTAATTTA-C
86190 TA-TTATCTATTTATTTA
1 TATTTATCTATTTATTTA
86207 CTATTATCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.15
27 45 0.75
28 6 0.10
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTTATCTATTTATTTATTAATTTAC
Found at i:86225 original size:19 final size:18
Alignment explanation
Indices: 86081--86226 Score: 79
Period size: 19 Copynumber: 7.9 Consensus size: 18
86071 ATTTATATTT
* *
86081 TTATTTATTAATTTAACTA
1 TTATCTATTTATTT-ACTA
86100 TTATCTATTTATTTACTA
1 TTATCTATTTATTTACTA
* * *
86118 TTTATATTTTTATTTATTAA
1 -TTATCTATTTATTTACT-A
*
86138 TTTAACTATTATCTATTTA-T-
1 -TTATCTA-T-T-TATTTACTA
86158 TTA-CTATTTATCTT--T-
1 TTATCTATTTAT-TTACTA
* *
86173 TTATTTATTAATTTAGCTA
1 TTATCTATTTATTTA-CTA
86192 TTATCTATTTATTTACTA
1 TTATCTATTTATTTACTA
*
86210 TTATCTACTTTTTTTAC
1 TTATCTA-TTTATTTAC
86227 CTACCTATTT
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
15 9 0.09
16 9 0.09
17 1 0.01
18 18 0.18
19 50 0.49
20 6 0.06
21 1 0.01
22 2 0.02
23 6 0.06
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATCTATTTATTTACTA
Found at i:86320 original size:12 final size:12
Alignment explanation
Indices: 86059--86315 Score: 116
Period size: 12 Copynumber: 22.6 Consensus size: 12
86049 AAGATTTTTT
86059 TATTTATTTA-C
1 TATTTATTTATC
*
86070 TATTTATATT-TT
1 TATTTAT-TTATC
* *
86082 TATTTATTAATT
1 TATTTATTTATC
**
86094 TAACTA-TTATC
1 TATTTATTTATC
86105 TATTTATTTA-C
1 TATTTATTTATC
*
86116 TATTTATATT-TT
1 TATTTAT-TTATC
* *
86128 TATTTATTAATT
1 TATTTATTTATC
**
86140 TAACTA-TTATC
1 TATTTATTTATC
86151 TATTTATTTA-C
1 TATTTATTTATC
*
86162 TATTTATCTT-TT
1 TATTTAT-TTATC
* *
86174 TATTTATTAATT
1 TATTTATTTATC
**
86186 TAGCTA-TTATC
1 TATTTATTTATC
86197 TATTTATTTA-C
1 TATTTATTTATC
*
86208 TA-TTATCTA-C
1 TATTTATTTATC
*
86218 T-TTT-TTTACC
1 TATTTATTTATC
**
86228 TACCTATTTATC
1 TATTTATTTATC
* * *
86240 TAATTATCTATA
1 TATTTATTTATC
**
86252 TACCTATTTATC
1 TATTTATTTATC
*
86264 TTTTTATTTATC
1 TATTTATTTATC
86276 TA-TTATTT-TC
1 TATTTATTTATC
* *
86286 -ACTTATTTTTC
1 TATTTATTTATC
*
86297 TATTTATTTATT
1 TATTTATTTATC
86309 TATTTAT
1 TATTTAT
86316 CTATTACTTT
Statistics
Matches: 183, Mismatches: 44, Indels: 37
0.69 0.17 0.14
Matches are distributed among these distances:
9 4 0.02
10 20 0.11
11 59 0.32
12 100 0.55
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATTTATC
Found at i:89338 original size:20 final size:22
Alignment explanation
Indices: 89305--89350 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
89295 AAGAAAAATG
89305 AAGAAAAGAATTGAAAAAG-AA
1 AAGAAAAGAATTGAAAAAGCAA
*
89326 AAGAAAA-AGTTGAAAAAGCAA
1 AAGAAAAGAATTGAAAAAGCAA
89347 AAGA
1 AAGA
89351 CGGAGGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (22 bp):
AAGAAAAGAATTGAAAAAGCAA
Found at i:90921 original size:52 final size:52
Alignment explanation
Indices: 90803--90960 Score: 176
Period size: 52 Copynumber: 3.0 Consensus size: 52
90793 AAATCTAAGC
* *
90803 CCTGG-GCGGTCTTTCATAGAAGCTTTCAGAGATCTAAGTTGATTTTAAGATGA
1 CCTGGTGCGGTCTTTCATAGAAGCTTTCAGAGA--TAAGTTGATCTTCAGATGA
*
90856 CCTTGTGCGGTCTTTCATAGAAGCTTTCAGAGATAAGTTGATCTTCAGATGA
1 CCTGGTGCGGTCTTTCATAGAAGCTTTCAGAGATAAGTTGATCTTCAGATGA
** * * * *
90908 -CTCGGTGTTGTCTTTCATAGAAGTTTTTAGACATCAGAGTTGATCCTCAGATG
1 CCT-GGTGCGGTCTTTCATAGAAGCTTTCAGAGAT-A-AGTTGATCTTCAGATG
90961 GTCTAGTGAG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
51 2 0.02
52 42 0.46
53 5 0.05
54 42 0.46
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (52 bp):
CCTGGTGCGGTCTTTCATAGAAGCTTTCAGAGATAAGTTGATCTTCAGATGA
Found at i:90984 original size:54 final size:54
Alignment explanation
Indices: 90926--91258 Score: 386
Period size: 54 Copynumber: 6.2 Consensus size: 54
90916 TGTCTTTCAT
* * * * *
90926 AGAAGTTTTTAGACATCAGAGTTGATCCTCAGATGGTCTAGTGAGATCATTCCA
1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
* *
90980 AGAAGTTTTGA-ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCA
1 AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
** * ** *
91034 AGAAGTTTTCT-TTGATCAGAGTTGAT-TCCAGATGGCCCAGTGCGATCATTCCT
1 AGAAGTTTT-TAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
* * * *
91087 ATAAG-TTTTAGAGATCAGAATTGATCCCTAGATGATCCAGTGCGATCATTCAAA
1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTC-CA
* * * *
91141 AGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGTGTGGTCATTCCA
1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
* * *
91195 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGAACCGGTGCGGTCATTCCA
1 AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
*
91249 TGAAGTTTTT
1 AGAAGTTTTT
91259 TTTATAATCA
Statistics
Matches: 234, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
51 1 0.00
52 15 0.06
53 48 0.21
54 130 0.56
55 40 0.17
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (54 bp):
AGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGATCATTCCA
Found at i:91165 original size:161 final size:161
Alignment explanation
Indices: 90927--91257 Score: 445
Period size: 161 Copynumber: 2.0 Consensus size: 161
90917 GTCTTTCATA
* * * * *
90927 GAAGTTTTTAGACATCAGAGTTGATCCTCAGATGGTCTAGTGAGATCATTCCAAGAAGTTTTGAA
1 GAAG-TTTTAGACATCAGAATTGATCCTCAGATGATCCAGTGAGATCATTCAAAGAAGTTTTCAA
**
90992 TGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCT-TTGATCAGAGT
65 TGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-TAGAGATCAGAGT
* **
91056 TGAT-TCCAGATGGCCCAGTGCGATCATTCCTAT
129 TGATCCCCAGATGAACCAGTGCGATCATTCC-AT
* *
91089 -AAGTTTTAGAGATCAGAATTGATCC-CTAGATGATCCAGTGCGATCATTCAAAAGAAGTTTTCA
1 GAAGTTTTAGACATCAGAATTGATCCTC-AGATGATCCAGTGAGATCATTC-AAAGAAGTTTTCA
* *
91152 GTGATCAGAGTTGATCCCCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTTAGAGATCAGAGT
64 ATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGT
* *
91217 TGATCCCCAGATGAACCGGTGCGGTCATTCCAT
129 TGATCCCCAGATGAACCAGTGCGATCATTCCAT
91250 GAAGTTTT
1 GAAGTTTT
91258 TTTTATAATC
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
159 1 0.01
160 40 0.27
161 79 0.53
162 28 0.19
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (161 bp):
GAAGTTTTAGACATCAGAATTGATCCTCAGATGATCCAGTGAGATCATTCAAAGAAGTTTTCAAT
GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTG
ATCCCCAGATGAACCAGTGCGATCATTCCAT
Found at i:91373 original size:34 final size:34
Alignment explanation
Indices: 91257--91739 Score: 579
Period size: 34 Copynumber: 13.6 Consensus size: 34
91247 CATGAAGTTT
* *
91257 TTTTTATAATCAGAGTTGATCTCGTTTCAAGAAG
1 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
91291 TTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 --TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
91327 TTTTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
1 ---TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
91364 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
1 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
*
91398 TTTTTATGATCAGAGTTGATCTCCTTTCAAGAAG
1 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* * *
91432 TTTTCGATTATCAGAGTTGTTCTCATTTCAAGAAGG
1 TTTT-TATGATCAGAGTTGATCTCATTTCAAGAA-G
*
91468 TTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAG
1 ---TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
91505 TTTTCGATGATCAGAGTTGATTTCATTTCAAGAAG
1 TTTT-TATGATCAGAGTTGATCTCATTTCAAGAAG
91540 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
1 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* * * *
91574 TTTTCCAATGATTAAAGTTGATCTCCTTTCAAGAAG
1 TTTT--TATGATCAGAGTTGATCTCATTTCAAGAAG
* *
91610 TTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAG
1 TTTT-TATGATCAGAGTTGATCTCATTTCAAGAAG
* * *
91645 TTTTGATGATCAGAGTTGATTTTATTTCAAGAAG
1 TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* * *
91679 TTTTTTTTATGATCAGATTTGATCTTATTTTTAAGAAG
1 ---TTTTTATGATCAGAGTTGATCTCA-TTTCAAGAAG
*
91717 TTTTCGATGATCAGAGTTGATCT
1 TTTT-TATGATCAGAGTTGATCT
91740 TCAAAAGAAA
Statistics
Matches: 398, Mismatches: 35, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
34 133 0.33
35 91 0.23
36 79 0.20
37 57 0.14
38 34 0.09
39 4 0.01
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (34 bp):
TTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
Found at i:91473 original size:105 final size:104
Alignment explanation
Indices: 91256--91739 Score: 630
Period size: 107 Copynumber: 4.6 Consensus size: 104
91246 CCATGAAGTT
* * **
91256 TTTTTTATAATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTTATGATCAGAGTTGATCTCCTTTC
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTCCTTTC
* *
91321 AAGAAGTTTTTTTTATGATCAGAGTTGATCTCGTTTCAAGAAG
65 AAGAAG---TTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
*
91364 -TTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTTCA
1 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTTCA
* *
91427 AGAAGTTTTCGATTATCAGAGTTGTTCTCATTTCAAGAAGG
66 AGAAGTTTT-GATGATCAGAGTTGATCTCATTTCAAGAA-G
* * *
91468 TTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATTTCATTT
1 --TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTT
*
91533 CAAGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
64 CAAGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
** * * * *
91574 TTTTCCAATGATTAAAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
1 TTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTTC
* *
91639 AAGAAGTTTTGATGATCAGAGTTGATTTTATTTCAAGAAG
65 AAGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
* * *
91679 TTTTTTTTATGATCAGATTTGATCTTATTTTTAAGAAGTTTTCGATGATCAGAGTTGATCT
1 --TTTTTTATGATCAGAGTTGATCTCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
91740 TCAAAAGAAA
Statistics
Matches: 334, Mismatches: 32, Indels: 21
0.86 0.08 0.05
Matches are distributed among these distances:
102 4 0.01
103 25 0.07
104 5 0.01
105 119 0.36
106 19 0.06
107 131 0.39
108 31 0.09
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (104 bp):
TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCCTTTCA
AGAAGTTTTGATGATCAGAGTTGATCTCATTTCAAGAAG
Found at i:92964 original size:4 final size:4
Alignment explanation
Indices: 92955--93234 Score: 93
Period size: 4 Copynumber: 70.8 Consensus size: 4
92945 AAAAAAGATT
* * **
92955 TTTA TTTA TTTA -CTA TTTA TATT- TTTA TTTA TTAA TTTA ACTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * **
93001 TCTA TTTA TTTA -CTA TTTA TATT- TTTA TTTA TTAA TTTA ACTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * **
93047 TCTA TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTAA TTTA GCTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * ** ** * *
93093 TCTA TTTA TTTA CTATTA TCTA CTTTT TTTA CCTA CCTA TTTA TCTA ATTA
1 TTTA TTTA TTTA -T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * ** * *
93144 TCTA TATA CCTA TTTA TCTT- TTTA TTTA TCTA -TTA TTTTCA CTTA TTT-
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA
*
93192 TTCTA TTTA TTTA TTTA TTTA TTTA TATA -TTA CTTT- TTTA TTT
1 TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT
93235 TAATATTTTT
Statistics
Matches: 200, Mismatches: 51, Indels: 50
0.66 0.17 0.17
Matches are distributed among these distances:
3 29 0.14
4 147 0.74
5 20 0.10
6 4 0.02
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:92983 original size:19 final size:19
Alignment explanation
Indices: 92959--93077 Score: 72
Period size: 19 Copynumber: 6.4 Consensus size: 19
92949 AAGATTTTTA
92959 TTTATTTACTATTTATATT
1 TTTATTTACTATTTATATT
* *
92978 TTTATTTATTAATTTA-ACT
1 TTTATTTACT-ATTTATATT
*
92997 ATTA--T-CTATTTAT-TT
1 TTTATTTACTATTTATATT
** *
93012 ACTATTTA-TATTTTTATT
1 TTTATTTACTATTTATATT
* *
93030 TATTAATTTAACTA-TTATCTA
1 T-TT-ATTT-ACTATTTATATT
*
93051 TTTATTTACTATTTATCTT
1 TTTATTTACTATTTATATT
93070 TTTATTTA
1 TTTATTTA
93078 TTAATTTAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
15 9 0.12
16 1 0.01
17 8 0.11
18 6 0.08
19 33 0.43
20 11 0.14
21 6 0.08
22 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTACTATTTATATT
Found at i:92992 original size:27 final size:26
Alignment explanation
Indices: 92955--93039 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
92945 AAAAAAGATT
92955 TTTATTTATTTACTATTTATATTTTTA
1 TTTA-TTATTTACTATTTATATTTTTA
* *
92982 TTTATTAATTTAACTA-TTATCTATTTA
1 TTTATT-ATTT-ACTATTTATATTTTTA
* *
93009 TTTACTATTTA-TATTTTTATTTATTAA
1 TTTATTATTTACTATTTATATTT-TT-A
93036 TTTA
1 TTTA
93040 ACTATTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
24 2 0.04
25 6 0.13
26 8 0.17
27 27 0.57
28 4 0.09
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATTATTTACTATTTATATTTTTA
Found at i:93024 original size:46 final size:46
Alignment explanation
Indices: 92957--93109 Score: 288
Period size: 46 Copynumber: 3.3 Consensus size: 46
92947 AAAAGATTTT
92957 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
93003 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
* *
93049 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
93095 TATTTATTTACTATT
1 TATTTATTTACTATT
93110 ATCTACTTTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
Found at i:93047 original size:27 final size:27
Alignment explanation
Indices: 92998--93085 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
92988 AATTTAACTA
* * *
92998 TTATCTATTTATTTACTATTTATATTT
1 TTATTTATTAATTTACTATTTATATAT
*
93025 TTATTTATTAATTTAACTA-TTATCTAT
1 TTATTTATTAATTT-ACTATTTATATAT
* * *
93052 TTATTTACT-ATTTATCTTTTTATTTAT
1 TTATTTATTAATTTA-CTATTTATATAT
*
93079 TAATTTA
1 TTATTTA
93086 GCTATTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 39 0.78
28 4 0.08
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTAATTTACTATTTATATAT
Found at i:93093 original size:27 final size:27
Alignment explanation
Indices: 93007--93104 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
92997 ATTATCTATT
* *
93007 TATTTA-CTATTTATATT-TTTATTTAT
1 TATTTATCTATTTAT-TTATTAATTTAC
* * *
93033 TAATTTAACTA-TTATCTATTTATTTAC
1 T-ATTTATCTATTTATTTATTAATTTAC
*
93060 TATTTATCTTTTTATTTATTAATTTAGC
1 TATTTATCTATTTATTTATTAATTTA-C
93088 TA-TTATCTATTTATTTA
1 TATTTATCTATTTATTTA
93105 CTATTATCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.15
27 45 0.75
28 6 0.10
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTTATCTATTTATTTATTAATTTAC
Found at i:93123 original size:19 final size:18
Alignment explanation
Indices: 92979--93124 Score: 79
Period size: 19 Copynumber: 7.9 Consensus size: 18
92969 ATTTATATTT
* *
92979 TTATTTATTAATTTAACTA
1 TTATCTATTTATTT-ACTA
92998 TTATCTATTTATTTACTA
1 TTATCTATTTATTTACTA
* * *
93016 TTTATATTTTTATTTATTAA
1 -TTATCTATTTATTTACT-A
*
93036 TTTAACTATTATCTATTTA-T-
1 -TTATCTA-T-T-TATTTACTA
93056 TTA-CTATTTATCTT--T-
1 TTATCTATTTAT-TTACTA
* *
93071 TTATTTATTAATTTAGCTA
1 TTATCTATTTATTTA-CTA
93090 TTATCTATTTATTTACTA
1 TTATCTATTTATTTACTA
*
93108 TTATCTACTTTTTTTAC
1 TTATCTA-TTTATTTAC
93125 CTACCTATTT
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
15 9 0.09
16 9 0.09
17 1 0.01
18 18 0.18
19 50 0.49
20 6 0.06
21 1 0.01
22 2 0.02
23 6 0.06
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATCTATTTATTTACTA
Found at i:93222 original size:12 final size:12
Alignment explanation
Indices: 92957--93222 Score: 125
Period size: 12 Copynumber: 23.3 Consensus size: 12
92947 AAAAGATTTT
92957 TATTTATTTA-C
1 TATTTATTTATC
*
92968 TATTTATATT-TT
1 TATTTAT-TTATC
* *
92980 TATTTATTAATT
1 TATTTATTTATC
**
92992 TAACTA-TTATC
1 TATTTATTTATC
93003 TATTTATTTA-C
1 TATTTATTTATC
*
93014 TATTTATATT-TT
1 TATTTAT-TTATC
* *
93026 TATTTATTAATT
1 TATTTATTTATC
**
93038 TAACTA-TTATC
1 TATTTATTTATC
93049 TATTTATTTA-C
1 TATTTATTTATC
*
93060 TATTTATCTT-TT
1 TATTTAT-TTATC
* *
93072 TATTTATTAATT
1 TATTTATTTATC
**
93084 TAGCTA-TTATC
1 TATTTATTTATC
93095 TATTTATTTA-C
1 TATTTATTTATC
*
93106 TA-TTATCTA-C
1 TATTTATTTATC
*
93116 T-TTT-TTTACC
1 TATTTATTTATC
**
93126 TACCTATTTATC
1 TATTTATTTATC
* * *
93138 TAATTATCTATA
1 TATTTATTTATC
**
93150 TACCTATTTATC
1 TATTTATTTATC
*
93162 TTTTTATTTATC
1 TATTTATTTATC
93174 TA-TTATTT-TC
1 TATTTATTTATC
* *
93184 -ACTTATTTTTC
1 TATTTATTTATC
*
93195 TATTTATTTATT
1 TATTTATTTATC
*
93207 TATTTATTTATA
1 TATTTATTTATC
93219 TATT
1 TATT
93223 ACTTTTTTAT
Statistics
Matches: 191, Mismatches: 45, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.02
10 20 0.10
11 59 0.31
12 108 0.57
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATTTATC
Found at i:96327 original size:26 final size:27
Alignment explanation
Indices: 96273--96349 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
96263 AATGACCGAG
* *
96273 ATGCCCTTG-ACTATGCAAAATAACCAAA
1 ATGCCCTTGAAC-ATGC-AAATGACAAAA
* *
96301 ATGCCC-TGGACGTGCAAATGACAAAA
1 ATGCCCTTGAACATGCAAATGACAAAA
96327 ATGCCCTTGAACATGCAAATGAC
1 ATGCCCTTGAACATGCAAATGAC
96350 CCAAAGTGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 15 0.36
27 19 0.45
28 8 0.19
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (27 bp):
ATGCCCTTGAACATGCAAATGACAAAA
Found at i:96343 original size:27 final size:26
Alignment explanation
Indices: 96273--96349 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
96263 AATGACCGAG
* *
96273 ATGCCCTTGACTATGCAAAATAACCAAA
1 ATGCCCTTGAC-ATGC-AAATGACAAAA
* *
96301 ATGCCCTGGACGTGCAAATGACAAAA
1 ATGCCCTTGACATGCAAATGACAAAA
96327 ATGCCCTTGAACATGCAAATGAC
1 ATGCCCTTG-ACATGCAAATGAC
96350 CCAAAGTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.40
27 15 0.36
28 10 0.24
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (26 bp):
ATGCCCTTGACATGCAAATGACAAAA
Found at i:103919 original size:40 final size:40
Alignment explanation
Indices: 103864--103945 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
103854 GTTAACTATG
103864 AATGCAGCCAGTAAGTGCAAAATCATATTCTCACATCTAC
1 AATGCAGCCAGTAAGTGCAAAATCATATTCTCACATCTAC
*
103904 AATGCAGCCAGTAAGTGCAAAATCATCTTCTCACATCTAC
1 AATGCAGCCAGTAAGTGCAAAATCATATTCTCACATCTAC
103944 AA
1 AA
103946 ATTCAATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (40 bp):
AATGCAGCCAGTAAGTGCAAAATCATATTCTCACATCTAC
Found at i:107249 original size:33 final size:31
Alignment explanation
Indices: 107197--107259 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 31
107187 ACATGACACG
107197 TTTTTTTTTTTGCCATAACATGACACGTTTT
1 TTTTTTTTTTTGCCATAACATGACACGTTTT
*
107228 TTTTTTTTTTTGGCATCTAACATGACACGTTT
1 TTTTTTTTTTTGCCA--TAACATGACACGTTT
107260 AAAAAGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 14 0.48
33 15 0.52
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (31 bp):
TTTTTTTTTTTGCCATAACATGACACGTTTT
Found at i:111657 original size:24 final size:25
Alignment explanation
Indices: 111611--111658 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
111601 GAGTGATGAA
*
111611 GAGGAGCAAAGAGAAAAGGGGAGAT
1 GAGGAGCAAAGAGAAAAGAGGAGAT
111636 GAGGAG-AAAGA-AAAAGAAGGAGA
1 GAGGAGCAAAGAGAAAAG-AGGAGA
111659 AAACAGAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 10 0.48
25 6 0.29
ACGTcount: A:0.54, C:0.02, G:0.42, T:0.02
Consensus pattern (25 bp):
GAGGAGCAAAGAGAAAAGAGGAGAT
Found at i:114443 original size:228 final size:228
Alignment explanation
Indices: 114043--114499 Score: 860
Period size: 228 Copynumber: 2.0 Consensus size: 228
114033 GCACCAATGT
*
114043 TAGGAGCGAAGGAAATTTAGGAAGAAAGAAATAGGAAGAAATAGATGGACAGAGCACAGAAAGAA
1 TAGGAGCGAAGGAAATTTAGGAAGAAAGAAATAGGAAGAAATAGATGGACAGAACACAGAAAGAA
*
114108 GAGAATAGAAATTTTAGATGAAAAAATATTACTTCTTGTTACAAACTGATTTACAACGTGGGTAT
66 GAGAATAGAAATTTTAGATGAAAAAATATTACTTCTTGTTACAAACCGATTTACAACGTGGGTAT
*
114173 ATAAAGAGATGTGTTCAAGGATAACTACCTAGAGTTATTGCCTAGAATCATGCCACTAACAAGAG
131 ATAAAGAGATGTGTTCAAGGATAACTACCTAGAGTGATTGCCTAGAATCATGCCACTAACAAGAG
114238 TTGTGCAAAAGGAAATAACTGAAACAAAATAAC
196 TTGTGCAAAAGGAAATAACTGAAACAAAATAAC
*
114271 TAGGAGCGAAGGAAATTTAGGAAGAAAGAAATAGGAAGAAATAGATGGACAGAACAGAGAAAGAA
1 TAGGAGCGAAGGAAATTTAGGAAGAAAGAAATAGGAAGAAATAGATGGACAGAACACAGAAAGAA
* *
114336 GAGAATAGAAATTTTAGATGAGAAAATATTACTTCTTGTTACAAACCGGTTTACAACGTGGGTAT
66 GAGAATAGAAATTTTAGATGAAAAAATATTACTTCTTGTTACAAACCGATTTACAACGTGGGTAT
114401 ATAAAGAGATGTGTTCAAGGATAACTACCTAGAGTGATTGCCTAGAATCATGCCACTAACAAGAG
131 ATAAAGAGATGTGTTCAAGGATAACTACCTAGAGTGATTGCCTAGAATCATGCCACTAACAAGAG
114466 TTGTGCAAAAGGAAATAACTGAAACAAAATAAC
196 TTGTGCAAAAGGAAATAACTGAAACAAAATAAC
114499 T
1 T
114500 TAAAGAAAAT
Statistics
Matches: 223, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
228 223 1.00
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (228 bp):
TAGGAGCGAAGGAAATTTAGGAAGAAAGAAATAGGAAGAAATAGATGGACAGAACACAGAAAGAA
GAGAATAGAAATTTTAGATGAAAAAATATTACTTCTTGTTACAAACCGATTTACAACGTGGGTAT
ATAAAGAGATGTGTTCAAGGATAACTACCTAGAGTGATTGCCTAGAATCATGCCACTAACAAGAG
TTGTGCAAAAGGAAATAACTGAAACAAAATAAC
Done.